TheCellVision

SMD1

Standard name	SMD1 ORF YGR074W Aliases mRNA splicing protein SMD1, SPP92
Human Ortholog	SNRPD1
Description	Core Sm protein Sm D1; part of heteroheptameric complex (with Smb1p, Smd2p, Smd3p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; relocalizes to the cytosol in response to hypoxia; homolog of human Sm D1; protein abundance increases in response to DNA replication stress

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Scale images

smd1-1

Micrographs

Sub-cellular Localization

LOC-score
Cell count

	ensLOC																		DeepLoc
Localization	WT1	WT2	WT3	RAP60	RAP140	RAP220	RAP300	RAP380	RAP460	RAP540	RAP620	RAP700	HU80	HU120	HU160	rpd3Δ_1	rpd3Δ_2	rpd3Δ_3	WT1	WT2	WT3	AF100	AF140	AF180
Cortical Patches	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Bud	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Bud Neck	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Bud Site	0	0	0	0	0	0	–	0	0	0	0	0.05	0	0	0	0	0	0	–	–	–	–	–	–
Cell Periphery	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Cytoplasm	0	0	0	0	0.06	0	–	0	0	0	0	0	0.07	0.12	0.15	0.05	0.13	0.07	0	0	0	0	0	0
Endoplasmic Reticulum	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Endosome	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Golgi	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Mitochondria	0	0	0.07	0.07	0.06	0.08	–	0.08	0.17	0.13	0.15	0.16	0	0	0	0	0	0	0	0	0	0	0	0
Nucleus	0.94	0.92	0.9	0.9	0.8	0.83	–	0.73	0.74	0.75	0.74	0.74	0.88	0.82	0.77	0.87	0.78	0.88	0.94	0.91	0.88	0.8	0.72	0.64
Nuclear Periphery	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Nucleolus	0.08	0.09	0.15	0.11	0.16	0.25	–	0.34	0.39	0.39	0.38	0.34	0.06	0.06	0.06	0.06	0.05	0	0	0	0	0.07	0.12	0.13
Peroxisomes	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
SpindlePole	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Vac/Vac Membrane	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.08	0.12	0.17

	ensLOC																		DeepLoc
Localization	WT1	WT2	WT3	RAP60	RAP140	RAP220	RAP300	RAP380	RAP460	RAP540	RAP620	RAP700	HU80	HU120	HU160	rpd3Δ_1	rpd3Δ_2	rpd3Δ_3	WT1	WT2	WT3	AF100	AF140	AF180
Cortical Patches	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Bud	0	0	1	0	1	1	–	1	0	3	2	2	0	2	1	0	0	0	3	1	1	2	1	6
Bud Neck	0	0	0	0	0	0	–	3	0	3	0	0	0	0	1	0	0	0	0	0	1	0	0	0
Bud Site	0	0	0	1	2	5	–	15	6	20	12	23	0	4	0	2	2	1	–	–	–	–	–	–
Cell Periphery	0	0	0	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Cytoplasm	10	8	12	17	30	10	–	21	6	7	7	8	25	66	85	15	25	21	0	2	2	0	2	2
Endoplasmic Reticulum	0	0	0	0	0	0	–	0	0	0	0	0	0	0	1	3	1	3	0	0	0	0	0	1
Endosome	1	0	1	0	3	0	–	0	0	0	0	0	2	0	4	3	1	1	4	0	5	2	2	2
Golgi	0	0	0	0	0	0	–	0	0	0	0	0	1	0	0	1	1	0	2	0	1	1	0	1
Mitochondria	13	1	36	29	28	60	–	70	69	95	67	80	1	3	0	8	8	5	4	2	0	0	4	5
Nucleus	518	209	494	354	408	591	–	631	299	538	323	369	306	456	450	275	149	271	550	221	500	200	287	301
Nuclear Periphery	1	1	3	4	4	8	–	8	3	12	4	8	1	4	3	2	2	0	1	0	0	0	0	1
Nucleolus	43	21	83	42	80	177	–	291	156	284	168	169	22	36	36	18	10	9	7	5	24	18	46	63
Peroxisomes	1	0	0	0	0	0	–	0	0	0	0	0	0	5	10	2	0	0	0	0	0	0	0	0
SpindlePole	0	0	1	0	1	1	–	1	0	0	0	1	2	15	18	0	0	0	1	0	3	1	1	1
Vac/Vac Membrane	2	4	7	0	11	4	–	11	1	7	5	5	5	2	11	8	6	11	12	5	17	20	47	80
Unique Cell Count	551	228	546	394	508	712		863	405	721	439	500	346	554	584	315	192	309	588	243	567	250	398	471
Labelled Cell Count	589	244	638	447	568	857		1052	540	969	588	665	365	593	620	337	205	322	588	243	567	250	398	471

Yeast GFP Assignment

Nucleus

(Huh et al. Nature 2003 425:686)

Protein Abundance

Screen	WT1	WT2	WT3	RAP60	RAP140	RAP220	RAP300	RAP380	RAP460	RAP540	RAP620	RAP700	HU80	HU120	HU160	rpd3Δ_1	rpd3Δ_2	rpd3Δ_3	AF100	AF140	AF180
Mean Cell GFP Intensity (1e^-4)	10.0	12.9	8.1	9.4	9.9	8.0	–	8.5	7.9	7.9	8.1	7.9	11.3	12.2	11.8	12.8	12.0	12.5	11.7	12.6	12.7
Std Deviation (1e^-4)	2.8	3.5	2.6	3.9	4.7	2.8	–	3.2	3.3	3.0	3.2	2.9	3.8	4.5	4.8	4.7	4.6	4.8	2.8	3.1	2.9
Intensity Change (Log₂)	–	–	–	0.22	0.29	-0.02	–	0.07	-0.04	-0.04	0.0	-0.04	0.48	0.59	0.54	0.66	0.57	0.63	0.54	0.64	0.64

Localization Change

Localization	RAP60	RAP140	RAP220	RAP300	RAP380	RAP460	RAP540	RAP620	RAP700	HU80	HU120	HU160	rpd3Δ_1	rpd3Δ_2	rpd3Δ_3
Cortical Patches	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0
Bud	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0
Bud Neck	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0
Bud Site	0	0	0	–	3.1	0	3.9	3.9	5.1	0	0	0	0	0	0
Cell Periphery	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0
Cytoplasm	1.9	3.1	-1.1	–	0.3	-0.8	-1.8	-0.7	-0.7	3.7	6.3	7.4	2.1	5.9	3.4
Endoplasmic Reticulum	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0
Endosome	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0
Golgi	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0
Mitochondria	0.5	-0.7	1.2	–	1.1	5.1	3.8	4.4	4.8	-4.6	-5.4	-6.3	-2.6	-1.2	-3.3
Nucleus	-0.3	-4.7	-3.8	–	-7.9	-6.8	-7.2	-7.0	-7.1	-1.0	-3.9	-6.1	-1.5	-4.6	-1.3
Nuclear Periphery	0	0	0	–	0	0	1.8	0	1.7	0	0	0	0	0	0
Nucleolus	-2.0	0.2	4.2	–	7.7	8.2	9.4	8.3	7.0	-4.0	-4.6	-4.9	-4.2	-3.6	-5.6
Peroxisomes	0	0	0	–	0	0	0	0	0	0	0	0	0	0	0
SpindlePole	0	0	0	–	0	0	0	0	0	0	3.5	3.8	0	0	0
Vacuole	0	1.1	0	–	0	0	-0.5	-0.2	-0.4	0	0	0.8	1.4	0	2.2

External localization resources

dHITS | Loqate | YeastGFP | YeastRGB | YeastRC

Images

Protein Concentration and Protein Localization Data

	R1						R2						R3
	G1 Pre-START	G1 Post-START	S/G2	Metaphase	Anaphase	Telophase	G1 Pre-START	G1 Post-START	S/G2	Metaphase	Anaphase	Telophase	G1 Pre-START	G1 Post-START	S/G2	Metaphase	Anaphase	Telophase
Concentration	9.6943	11.3169	9.7532	9.6872	8.7125	9.477	9.1754	8.2872	7.9874	7.762	7.232	7.8676	10.8895	11.3334	10.7167	10.0933	9.8181	10.5995
Actin	0.0039	0.0008	0.0119	0.0026	0.0072	0	0.0001	0	0	0.0001	0	0	0.0091	0	0.0001	0.0016	0.0004	0
Bud	0.0008	0.0001	0.0003	0.0001	0.0002	0.0001	0	0	0	0.0001	0	0	0.0002	0	0.0001	0.0005	0.0007	0
Bud Neck	0.0014	0.0001	0.0002	0	0.0003	0.0004	0	0	0	0.0002	0.0001	0.0004	0.0006	0	0.0001	0.0002	0.0005	0.0003
Bud Periphery	0.0013	0.0001	0.0005	0.0002	0.0004	0.0001	0	0	0	0.0001	0	0.0001	0.0002	0	0.0001	0.0006	0.0005	0
Bud Site	0.0019	0.0008	0.0008	0.0003	0.0004	0.0001	0	0	0	0.0001	0	0	0.0008	0	0.0002	0.0008	0.0019	0
Cell Periphery	0.0007	0	0.0002	0.0001	0.0001	0.0001	0	0	0	0	0	0	0.0002	0	0.0002	0.0004	0.0006	0
Cytoplasm	0.0154	0.0003	0.0088	0.0001	0.0003	0	0	0	0	0.0001	0	0	0.0039	0	0.0077	0.0018	0.0075	0
Cytoplasmic Foci	0.022	0.0002	0.0047	0.009	0.0106	0.0001	0.0014	0	0	0	0	0	0.0144	0	0.0029	0.0017	0.0058	0
Eisosomes	0.0002	0	0.0001	0	0.0001	0	0	0	0	0	0	0	0.0002	0	0	0	0.0001	0
Endoplasmic Reticulum	0.0013	0.0002	0.0004	0.0001	0.0005	0	0	0	0	0	0	0	0.0013	0	0.0006	0.0007	0.0011	0
Endosome	0.0172	0.0013	0.0028	0.005	0.0383	0	0.0003	0	0	0	0	0	0.0079	0	0.002	0.0059	0.001	0
Golgi	0.0059	0.0006	0.0034	0.0089	0.0215	0	0.0003	0	0	0	0	0	0.0019	0	0.0002	0.0007	0.0002	0
Lipid Particles	0.0217	0.0012	0.0066	0.0325	0.0213	0	0.0043	0	0	0	0	0	0.0163	0	0.0027	0.0014	0.0052	0
Mitochondria	0.0171	0.0035	0.0055	0.0152	0.0653	0.0003	0.0007	0	0	0.0005	0.0002	0.0005	0.0021	0.0001	0.0011	0.003	0.0021	0.0001
None	0.0018	0	0.0008	0.0002	0.0002	0	0	0	0	0	0	0	0.006	0	0.0007	0.0005	0.0041	0
Nuclear Periphery	0.0097	0.0016	0.0037	0.0009	0.0035	0.0003	0.0007	0.0015	0.0003	0.0009	0.0006	0.0004	0.0149	0.0008	0.0057	0.0106	0.0055	0.0002
Nucleolus	0.0553	0.0113	0.0209	0.0094	0.117	0.1076	0.0199	0.0151	0.0086	0.0162	0.1459	0.0909	0.0522	0.011	0.0279	0.0418	0.1452	0.0639
Nucleus	0.7905	0.9771	0.9129	0.9079	0.7053	0.8877	0.9532	0.9831	0.9909	0.9808	0.8494	0.9073	0.836	0.9876	0.9373	0.9076	0.8065	0.9351
Peroxisomes	0.0054	0.0002	0.008	0.0043	0.0039	0	0.015	0	0	0	0	0	0.0035	0	0.0001	0.001	0.0002	0
Punctate Nuclear	0.0168	0.0002	0.0041	0.0005	0.0009	0.0028	0.0029	0.0001	0.0001	0.0003	0.0036	0.0002	0.0251	0.0004	0.006	0.0143	0.007	0.0001
Vacuole	0.0054	0.0002	0.0014	0.0008	0.0012	0.0002	0.0005	0	0	0.0002	0.0001	0.0001	0.0017	0	0.0024	0.0026	0.0025	0.0001
Vacuole Periphery	0.0041	0.0003	0.0019	0.002	0.0016	0.0001	0.0004	0	0	0.0002	0.0001	0.0001	0.0014	0	0.0018	0.0023	0.0013	0

Sequencing Data

	R1					R2
	G1 Post-START	S/G2	Metaphase	Anaphase	Telophase	G1 Post-START	S/G2	Metaphase	Anaphase	Telophase
Gene Expression	36.2797	40.2603	28.2151	26.1877	22.7081	55.0146	39.5763	28.2377	29.4797	27.0034
Translational Efficiency	1.552	1.7647	1.5759	2.065	2.3029	0.9734	1.506	2.1073	1.8741	1.9075

Hit Data

Dataset	Hit
Protein Concentration	✘
Protein Localization	✘
Gene Expression	✘
Translational Efficiency	✘

Proteome Dynamics

Micrographs

Cell Count

R1				R2				R1 & R2
WT	UBP2	UBP14	UBP2UBP14	WT	UBP2	UBP14	UBP2UBP14	WT	UBP2	UBP14	UBP2UBP14
424	1638	87	201	146	2060	440	1588	570	3698	527	1789

Protein Abundance

	R1				R2				R1 & R2
	WT	UBP2	UBP14	UBP2UBP14	WT	UBP2	UBP14	UBP2UBP14	WT	UBP2	UBP14	UBP2UBP14
Mean	957.57	1193.99	1301.11	1404.08	1119.44	1104.12	1377.21	1456.44	999.03	1143.93	1364.65	1450.56
Standard Deviation	159.22	224.38	241.10	301.79	255.27	207.47	203.07	284.24	201.34	219.71	211.72	286.74
Intensity Change Log ₂	—	0.318341	0.442293	0.552175	—	-0.019880	0.298971	0.379669	—	0.145940	0.366820	0.461769

Localization Score (DeepLoc)

	R1				R2				R1 & R2
	WT	UBP2	UBP14	UBP2UBP14	WT	UBP2	UBP14	UBP2UBP14	WT	UBP2	UBP14	UBP2UBP14
Actin	0.000370	0.000487	0.000973	0.000790	0.000777	0.000513	0.000622	0.000620	0.000474	0.000502	0.000680	0.000639
Bud Neck	0.001630	0.006035	0.007329	0.008851	0.003725	0.006917	0.009171	0.013125	0.002167	0.006526	0.008867	0.012645
Bud Site	0.000125	0.000460	0.000738	0.000675	0.000313	0.000959	0.000563	0.001189	0.000173	0.000738	0.000592	0.001132
Cell Periphery	0.000016	0.000060	0.000019	0.000043	0.000048	0.000146	0.000022	0.000095	0.000024	0.000108	0.000021	0.000090
Cytoplasm	0.000039	0.000333	0.000021	0.000490	0.000079	0.000349	0.000029	0.000778	0.000050	0.000342	0.000028	0.000745
Cytoplasmic Foci	0.000085	0.000094	0.000064	0.000025	0.000027	0.000411	0.000016	0.000660	0.000070	0.000271	0.000024	0.000589
Eisosomes	0.000037	0.000080	0.000089	0.000034	0.000071	0.000103	0.000065	0.000041	0.000046	0.000093	0.000069	0.000041
Endoplasmic Reticulum	0.001904	0.001850	0.001028	0.001031	0.001498	0.002788	0.000791	0.001034	0.001800	0.002373	0.000830	0.001034
Endosome	0.000165	0.000211	0.000021	0.000035	0.000021	0.000228	0.000015	0.000685	0.000128	0.000221	0.000016	0.000612
Golgi	0.000049	0.000107	0.000078	0.000059	0.000040	0.000091	0.000035	0.000781	0.000047	0.000098	0.000042	0.000700
Lipid Particles	0.000154	0.000038	0.000020	0.000011	0.000014	0.000243	0.000009	0.000120	0.000118	0.000152	0.000011	0.000108
Mitochondria	0.000444	0.001199	0.001520	0.002235	0.001365	0.001374	0.001164	0.003002	0.000680	0.001296	0.001223	0.002916
Mitotic Spindle	0.000214	0.002084	0.000089	0.000431	0.000025	0.001151	0.000027	0.001505	0.000165	0.001564	0.000038	0.001384
None	0.000714	0.000622	0.000517	0.002353	0.001648	0.001201	0.000491	0.000520	0.000953	0.000945	0.000496	0.000726
Nuclear Periphery	0.000023	0.000259	0.000044	0.000372	0.000041	0.000234	0.000047	0.000741	0.000028	0.000245	0.000046	0.000700
Nuclear Periphery Foci	0.000792	0.000344	0.000009	0.000025	0.000010	0.000300	0.000003	0.000399	0.000591	0.000319	0.000004	0.000357
Nucleolus	0.036466	0.031102	0.070414	0.019210	0.030824	0.030564	0.024533	0.016991	0.035021	0.030802	0.032107	0.017240
Nucleus	0.955480*	0.953108*	0.910997*	0.961968*	0.956721*	0.950566*	0.960895*	0.954297*	0.955798*	0.951692*	0.952658*	0.955159*
Peroxisomes	0.001057	0.000509	0.005542	0.000963	0.002396	0.000746	0.001187	0.000496	0.001400	0.000641	0.001906	0.000549
Vacuole	0.000134	0.000634	0.000334	0.000274	0.000252	0.000677	0.000223	0.001777	0.000164	0.000658	0.000241	0.001608
Vacuole Periphery	0.000101	0.000383	0.000155	0.000125	0.000103	0.000438	0.000092	0.001143	0.000102	0.000413	0.000103	0.001029

Localization Changes (T-score)

	R1					R2					R1 & R2
	UBP2_WT	UBP14_WT	UBP2UBP14_WT	UBP2UBP14_UBP2	UBP2UBP14_UBP14	UBP2_WT	UBP14_WT	UBP2UBP14_WT	UBP2UBP14_UBP2	UBP2UBP14_UBP14	UBP2_WT	UBP14_WT	UBP2UBP14_WT	UBP2UBP14_UBP2	UBP2UBP14_UBP14
Actin	-3.55	-7.12	-7.25	-5.65	1.18	4.11	1.82	1.80	-3.11	0.04	-0.79	-6.43	-5.41	-4.93	0.80
Bud Neck	-8.30	-5.11	-5.85	-2.88	-1.72	-3.34	-6.24	-8.03	-6.05	-3.44	-9.59	-11.33	-11.41	-6.95	-3.83
Bud Site	-4.58	-4.67	-3.23	-1.85	-0.61	-2.77	-3.94	-4.06	-1.00	-2.75	-4.32	-8.27	-5.14	-2.07	-2.77
Cell Periphery	-3.48	-1.29	-3.62	0.93	-2.93	-2.01	0.80	-1.47	1.07	-4.05	-3.59	0.15	-3.77	0.51	-4.22
Cytoplasm	-1.30	0.60	-3.40	-0.56	-3.53	-1.31	0.69	-1.18	-0.50	-1.26	-1.89	0.73	-1.33	-0.61	-1.36
Cytoplasmic Foci	-0.01	0.36	0.75	1.72	2.42	-1.71	1.76	-2.38	-0.75	-2.40	-1.33	0.80	-2.07	-1.20	-2.38
Eisosomes	-7.91	-6.28	0.16	7.85	6.30	-3.29	0.72	4.75	8.89	6.22	-9.27	-5.85	1.68	11.30	8.01
Endoplasmic Reticulum	0.26	3.73	4.52	4.38	0.03	-6.23	4.98	3.25	10.04	-3.15	-3.51	7.26	5.78	10.75	-2.73
Endosome	-0.06	0.94	0.82	2.07	-1.76	-3.11	0.44	-2.58	-1.68	-2.59	-0.44	0.98	-1.65	-1.62	-2.60
Golgi	-0.95	-0.73	-0.73	0.61	-0.03	-1.30	-0.25	-1.60	-1.48	-1.59	-1.23	0.11	-1.58	-1.45	-1.59
Lipid Particles	0.82	0.91	0.94	1.29	0.72	-1.48	1.37	-2.07	0.68	-2.14	-0.02	0.98	0.21	0.35	-2.11
Mitochondria	-2.71	-7.46	-6.68	-3.22	-2.75	0.03	0.75	-3.30	-2.81	-3.75	-2.46	-7.19	-5.32	-3.49	-3.94
Mitotic Spindle	-1.97	0.63	-1.08	0.12	-1.22	-2.11	-0.87	-2.43	-0.21	-2.41	-2.64	0.78	-2.27	0.04	-2.64
None	0.54	1.60	-2.88	-3.02	-3.25	0.42	1.15	1.14	2.46	-0.15	-0.03	1.60	0.73	1.17	-2.59
Nuclear Periphery	-2.44	-2.58	-3.60	-1.17	-3.36	-3.02	-1.37	-4.09	-2.82	-4.02	-3.90	-3.93	-4.45	-2.88	-4.29
Nuclear Periphery Foci	0.63	1.01	0.97	1.41	-1.76	-2.09	0.43	-2.85	-0.42	-2.86	0.55	1.01	0.52	-0.13	-2.89
Nucleolus	1.65	-3.05	2.73	1.83	4.10	0.14	0.89	3.31	6.01	2.99	1.69	0.26	6.32	6.92	4.82
Nucleus	0.58	3.76	0.33	-0.02	-3.27	1.28	-0.16	0.95	-0.27	1.32	1.30	1.40	1.02	-0.01	-0.41
Peroxisomes	1.85	-3.33	-0.02	-3.06	3.39	4.25	2.99	5.31	0.78	4.03	2.86	-1.55	3.02	0.08	5.06
Vacuole	-2.67	-3.12	-4.15	1.55	0.41	-3.00	0.19	-3.42	-2.37	-3.44	-4.27	-3.12	-3.67	-2.30	-3.41
Vacuole Periphery	-4.59	-2.39	-1.53	4.05	0.92	-4.89	0.42	-2.94	-1.94	-2.95	-6.50	-0.44	-2.96	-1.92	-2.94